I've got a TL Audio 5013 Parametric EQ going through my FX loop at the moment, but I wanna use the second channel of it as I'm only using the first. Would this work -

FX Loop Send - EQ Channel 1 input - EQ Channel 1 output into EQ Channel 2 input - Channel 2 output - FX Loop return.

Is this possible at all or would it destroy my EQ or amp!?
I think that you'll be fine, but I'm not 100%sure... I don't see why it wouldn't be ok.

Although, if both channels control the same frequencies, I think you'd get better use going

guitar -> channel 1 in of EQ
channel 1 out of EQ -> amp input
effects send-> EQ channel 2 in
EQ channel 2 out -> effects return

Thats what I'd do, at least..